Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2019 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #include "core/ActionAtomistic.h"
23 : #include "core/ActionPilot.h"
24 : #include "core/ActionRegister.h"
25 : #include "tools/Vector.h"
26 : #include "tools/AtomNumber.h"
27 : #include "tools/Tools.h"
28 : #include "core/Atoms.h"
29 : #include "core/PlumedMain.h"
30 : #include "core/ActionSet.h"
31 : #include "core/SetupMolInfo.h"
32 :
33 : #include <vector>
34 : #include <string>
35 : #include <limits>
36 :
37 : using namespace std;
38 :
39 : namespace PLMD {
40 : namespace generic {
41 :
42 : //+PLUMEDOC GENERIC WRAPAROUND
43 : /*
44 : Rebuild periodic boundary conditions around chosen atoms.
45 :
46 :
47 : Modify position of atoms indicated by ATOMS by shifting them by lattice vectors so that they are
48 : as close as possible to the atoms indicated by AROUND. More precisely, for every atom i
49 : in the ATOMS list the following procedure is performed:
50 : - The atom j among those in the AROUND list is searched that is closest to atom i.
51 : - The atom i is replaced with its periodic image that is closest to atom j.
52 :
53 : This action works similarly to \ref WHOLEMOLECULES in that it replaces atoms coordinate. Notice that only
54 : atoms specified with ATOMS are replaced, and that, at variance with \ref WHOLEMOLECULES,
55 : the order in which atoms are specified is irrelevant.
56 :
57 : This is often convenient at a post processing stage (using the \ref driver), but sometime
58 : it is required during the simulation if collective variables need atoms to be in a specific periodic image.
59 :
60 : \attention This directive modifies the stored position at the precise moment it is executed. This means that only collective variables which are below it in the input script will see the corrected positions. As a general rule, put it at the top of the input file. Also, unless you know exactly what you are doing, leave the default stride (1), so that this action is performed at every MD step.
61 :
62 : Consider that the computational cost grows with the product
63 : of the size of the two lists (ATOMS and AROUND), so that this action can become very expensive.
64 : If you are using it to analyse a trajectory this is usually not a big problem. If you use it to
65 : analyze a simulation on the fly, e.g. with \ref DUMPATOMS to store a properly wrapped trajectory,
66 : consider the possibility of using the STRIDE keyword here (with great care).
67 : \par Examples
68 :
69 : This command instructs plumed to move all the ions to their periodic image that is as close as possible to
70 : the rna group.
71 :
72 : \plumedfile
73 : rna: GROUP ATOMS=1-100
74 : ions: GROUP ATOMS=101-110
75 : # first make the rna molecule whole
76 : WHOLEMOLECULES ENTITY0=rna
77 : WRAPAROUND ATOMS=ions AROUND=rna
78 : DUMPATOMS FILE=dump.xyz ATOMS=rna,ions
79 : \endplumedfile
80 :
81 : In case you want to do it during a simulation and you only care about wrapping the ions in
82 : the `dump.xyz` file, you can use the following:
83 :
84 : \plumedfile
85 : # add some restraint that do not require molecules to be whole:
86 : a: TORSION ATOMS=1,2,10,11
87 : RESTRAINT ARG=a AT=0.0 KAPPA=5
88 :
89 :
90 : # then do the things that are required for dumping the trajectory
91 : # notice that they are all done every 100 steps, so as not to
92 : # unnecessarily overload the calculation
93 :
94 : rna: GROUP ATOMS=1-100
95 : ions: GROUP ATOMS=101-110
96 : # first make the rna molecule whole
97 : WHOLEMOLECULES ENTITY0=rna STRIDE=100
98 : WRAPAROUND ATOMS=ions AROUND=rna STRIDE=100
99 : DUMPATOMS FILE=dump.xyz ATOMS=rna,ions STRIDE=100
100 : \endplumedfile
101 :
102 : Notice that if the biased variable requires a molecule to be whole, you might have to put
103 : just the \ref WHOLEMOLECULES command before computing that variable and leave the default STRIDE=1.
104 :
105 : This command instructs plumed to center all atoms around the center of mass of a solute molecule.
106 :
107 : \plumedfile
108 : solute: GROUP ATOMS=1-100
109 : all: GROUP ATOMS=1-1000
110 : # center of the solute:
111 : # notice that since plumed 2.2 this also works if the
112 : # solute molecule is broken
113 : com: COM ATOMS=solute
114 : # notice that we wrap around a single atom. this should be fast
115 : WRAPAROUND ATOMS=all AROUND=com
116 : DUMPATOMS FILE=dump.xyz ATOMS=all
117 : \endplumedfile
118 :
119 : Notice that whereas \ref WHOLEMOLECULES is designed to make molecules whole,
120 : \ref WRAPAROUND can easily break molecules. In the last example,
121 : if solvent (atoms 101-1000) is made e.g. of water, then water
122 : molecules could be broken by \ref WRAPAROUND (hydrogen could end up
123 : in an image and oxygen in another one).
124 : One solution is to use \ref WHOLEMOLECULES on _all_ the water molecules
125 : after \ref WRAPAROUND. This is tedious. A better solution is to use the
126 : GROUPBY option which is going
127 : to consider the atoms listed in ATOMS as a list of groups
128 : each of size GROUPBY. The first atom of the group will be brought
129 : close to the AROUND atoms. The following atoms of the group
130 : will be just brought close to the first atom of the group.
131 : Assuming that oxygen is the first atom of each water molecules,
132 : in the following examples all the water oxygens will be brought
133 : close to the solute, and all the hydrogens will be kept close
134 : to their related oxygen.
135 :
136 : \plumedfile
137 : solute: GROUP ATOMS=1-100
138 : water: GROUP ATOMS=101-1000
139 : com: COM ATOMS=solute
140 : # notice that we wrap around a single atom. this should be fast
141 : WRAPAROUND ATOMS=solute AROUND=com
142 : # notice that we wrap around a single atom. this should be fast
143 : WRAPAROUND ATOMS=water AROUND=com GROUPBY=3
144 : DUMPATOMS FILE=dump.xyz ATOMS=solute,water
145 : \endplumedfile
146 :
147 : */
148 : //+ENDPLUMEDOC
149 :
150 :
151 8 : class WrapAround:
152 : public ActionPilot,
153 : public ActionAtomistic
154 : {
155 : vector<AtomNumber> atoms;
156 : vector<AtomNumber> reference;
157 : unsigned groupby;
158 : public:
159 : explicit WrapAround(const ActionOptions&ao);
160 : static void registerKeywords( Keywords& keys );
161 : void calculate();
162 10 : void apply() {}
163 : };
164 :
165 6454 : PLUMED_REGISTER_ACTION(WrapAround,"WRAPAROUND")
166 :
167 3 : void WrapAround::registerKeywords( Keywords& keys ) {
168 3 : Action::registerKeywords( keys );
169 3 : ActionAtomistic::registerKeywords( keys );
170 3 : ActionPilot::registerKeywords( keys );
171 15 : keys.add("compulsory","STRIDE","1","the frequency with which molecules are reassembled. Unless you are completely certain about what you are doing leave this set equal to 1!");
172 12 : keys.add("atoms","AROUND","reference atoms");
173 12 : keys.add("atoms","ATOMS","wrapped atoms");
174 15 : keys.add("compulsory","GROUPBY","1","group atoms so as not to break molecules");
175 3 : }
176 :
177 2 : WrapAround::WrapAround(const ActionOptions&ao):
178 : Action(ao),
179 : ActionPilot(ao),
180 : ActionAtomistic(ao),
181 6 : groupby(1)
182 : {
183 4 : parseAtomList("ATOMS",atoms);
184 4 : parseAtomList("AROUND",reference);
185 4 : parse("GROUPBY",groupby);
186 :
187 2 : log.printf(" atoms in reference :");
188 13 : for(unsigned j=0; j<reference.size(); ++j) log.printf(" %d",reference[j].serial() );
189 2 : log.printf("\n");
190 2 : log.printf(" atoms to be wrapped :");
191 658 : for(unsigned j=0; j<atoms.size(); ++j) log.printf(" %d",atoms[j].serial() );
192 2 : log.printf("\n");
193 2 : if(groupby>1) log<<" atoms will be grouped by "<<groupby<<"\n";
194 :
195 2 : if(atoms.size()%groupby!=0) error("number of atoms should be a multiple of groupby option");
196 :
197 2 : checkRead();
198 :
199 2 : if(groupby<=1) Tools::removeDuplicates(atoms);
200 2 : Tools::removeDuplicates(reference);
201 :
202 2 : vector<AtomNumber> merged(atoms.size()+reference.size());
203 : merge(atoms.begin(),atoms.end(),reference.begin(),reference.end(),merged.begin());
204 2 : Tools::removeDuplicates(merged);
205 2 : requestAtoms(merged);
206 : doNotRetrieve();
207 : doNotForce();
208 2 : }
209 :
210 10 : void WrapAround::calculate() {
211 1805 : for(unsigned i=0; i<atoms.size(); i+=groupby) {
212 : Vector & first (modifyPosition(atoms[i]));
213 : double mindist2=std::numeric_limits<double>::max();
214 : int closest=-1;
215 4625 : for(unsigned j=0; j<reference.size(); ++j) {
216 : Vector & second (modifyPosition(reference[j]));
217 1145 : Vector distance=pbcDistance(first,second);
218 1145 : double distance2=modulo2(distance);
219 1145 : if(distance2<mindist2) {
220 : mindist2=distance2;
221 875 : closest=j;
222 : }
223 : }
224 595 : plumed_massert(closest>=0,"closest not found");
225 595 : Vector & second (modifyPosition(reference[closest]));
226 : // place first atom of the group
227 595 : first=second+pbcDistance(second,first);
228 : // then place other atoms close to the first of the group
229 1585 : for(unsigned j=1; j<groupby; j++) {
230 495 : Vector & second (modifyPosition(atoms[i+j]));
231 495 : second=first+pbcDistance(first,second);
232 : }
233 : }
234 10 : }
235 :
236 :
237 :
238 : }
239 :
240 4839 : }
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